import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.ws.DBRefFetcher;
+import jalview.ws.phyre2.Phyre2Client;
+import jalview.ws.phyre2.Phyre2SummaryPojo;
import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Objects;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.table.AbstractTableModel;
/**
public class StructureChooser extends GStructureChooser implements
IProgressIndicator
{
- private boolean structuresDiscovered = false;
+ private static int MAX_QLENGTH = 7820;
private SequenceI selectedSequence;
private FTSRestClientI pdbRestCleint;
- private String selectedPdbFileName;
+ private String selectedStructureFileName;
private boolean isValidPBDEntry;
+ private boolean cachedPDBExists;
+
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ // ensure a filter option is in force for search
+ populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
.getString("status.searching_for_pdb_structures"),
startTime);
fetchStructuresMetaData();
- populateFilterComboBox();
+ // revise filter options if no results were found
+ populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(),
+ !chk_invertFilter.isSelected());
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
&& !discoveredStructuresSet.isEmpty())
{
getResultTable().setModel(
- FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet));
- structuresDiscovered = true;
+ JvSummaryTable.getTableModel(lastPdbRequest,
+ discoveredStructuresSet));
noOfStructuresFound = discoveredStructuresSet.size();
mainFrame.setTitle(MessageManager.formatMessage(
"label.structure_chooser_no_of_structures",
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
}
}
}
-
+ cachedPDBExists = !entries.isEmpty();
PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
tbl_local_pdb.setModel(tableModelx);
}
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
- HashSet<String> seqRefs = new LinkedHashSet<String>();
+ Set<String> seqRefs = new LinkedHashSet<String>();
- if (seq.getAllPDBEntries() != null)
+ if (seq.getAllPDBEntries() != null
+ && queryBuilder.length() < MAX_QLENGTH)
{
for (PDBEntry entry : seq.getAllPDBEntries())
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append("pdb_id")
- .append(":")
-.append(entry.getId().toLowerCase())
- .append(" OR ");
+ queryBuilder.append("pdb_id:")
+ .append(entry.getId().toLowerCase()).append(" OR ");
isPDBRefsFound = true;
- // seqRefs.add(entry.getId());
}
}
}
{
for (DBRefEntry dbRef : seq.getDBRefs())
{
- if (isValidSeqName(getDBRefId(dbRef)))
+ if (isValidSeqName(getDBRefId(dbRef))
+ && queryBuilder.length() < MAX_QLENGTH)
{
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
- queryBuilder
-.append("uniprot_accession").append(":")
- .append(getDBRefId(dbRef))
- .append(" OR ");
- queryBuilder
-.append("uniprot_id")
- .append(":")
+ queryBuilder.append("uniprot_accession:")
.append(getDBRefId(dbRef)).append(" OR ");
+ queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
+ .append(" OR ");
isUniProtRefsFound = true;
}
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append("pdb_id")
- .append(":").append(getDBRefId(dbRef).toLowerCase())
- .append(" OR ");
+ queryBuilder.append("pdb_id:")
+ .append(getDBRefId(dbRef).toLowerCase()).append(" OR ");
isPDBRefsFound = true;
}
else
.replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
-
/**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
getResultTable().setModel(
- FTSRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ JvSummaryTable.getTableModel(lastPdbRequest,
+ reorderedStructuresSet));
- FTSRestResponse.configureTableColumn(getResultTable(),
- wantedFields);
+ JvSummaryTable.configureTableColumn(getResultTable(),
+ wantedFields, tempUserPrefs);
getResultTable().getColumn("Ref Sequence").setPreferredWidth(120);
getResultTable().getColumn("Ref Sequence").setMinWidth(100);
getResultTable().getColumn("Ref Sequence").setMaxWidth(200);
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
+ JvOptionPane.showMessageDialog(
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
int value = chooser.showOpenDialog(null);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- selectedPdbFileName = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ selectedStructureFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedStructureFileName);
validateSelections();
}
}
* Populates the filter combo-box options dynamically depending on discovered
* structures
*/
- @Override
- protected void populateFilterComboBox()
+ protected void populateFilterComboBox(boolean haveData,
+ boolean cachedPDBExists)
{
- if (isStructuresDiscovered())
+ /*
+ * temporarily suspend the change listener behaviour
+ */
+ cmb_filterOption.removeItemListener(this);
+
+ cmb_filterOption.removeAllItems();
+ if (haveData)
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
- "overall_quality", VIEWS_FILTER));
+ "overall_quality", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- "resolution", VIEWS_FILTER));
+ "resolution", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- "number_of_protein_chains", VIEWS_FILTER));
+ "number_of_protein_chains", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- "number_of_bound_molecules", VIEWS_FILTER));
+ "number_of_bound_molecules", VIEWS_FILTER, false));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- "number_of_polymer_residues", VIEWS_FILTER));
+ "number_of_polymer_residues", VIEWS_FILTER, true));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
+ VIEWS_ENTER_ID, false));
cmb_filterOption.addItem(new FilterOption("From File", "-",
- VIEWS_FROM_FILE));
- cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
- VIEWS_LOCAL_PDB));
+ VIEWS_FROM_FILE, false));
+
+ if (cachedPDBExists)
+ {
+ FilterOption cachedOption = new FilterOption("Cached PDB Entries",
+ "-", VIEWS_LOCAL_PDB, false);
+ cmb_filterOption.addItem(cachedOption);
+ cmb_filterOption.setSelectedItem(cachedOption);
+ }
+
+ cmb_filterOption.addItem(new FilterOption(
+ "Predict 3D Model with Phyre2", "-", VIEWS_PHYRE2_PREDICTION,
+ false));
+ cmb_filterOption.addItemListener(this);
}
/**
* Updates the displayed view based on the selected filter option
*/
- @Override
protected void updateCurrentView()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
chk_invertFilter.setVisible(true);
filterResultSet(selectedFilterOpt.getValue());
}
+ else if (selectedFilterOpt.getView() == VIEWS_PHYRE2_PREDICTION)
+ {
+ mainFrame.setTitle(MessageManager
+ .getString("label.phyre2_model_prediction"));
+ phyre2InputAssSeqPanel.loadCmbAssSeq();
+ }
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
{
validateAssociationFromFile();
}
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
+ {
+ validateAssociationFromPhyre2();
+ if (getPhyreResultTable().getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
}
/**
"-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
- if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ if (selectedStructureFileName != null && selectedStructureFileName.length() > 0)
{
btn_view.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
+ /**
+ * Validates inputs for Phyre2 3D Model prediction
+ */
+ public void validateAssociationFromPhyre2()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) phyre2InputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_runPhyre2Prediction.setEnabled(true);
+ }
+ else
+ {
+ btn_runPhyre2Prediction.setEnabled(false);
+ }
+ }
+
@Override
public void cmbAssSeqStateChanged()
{
public void ok_ActionPerformed()
{
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ final int preferredHeight = pnl_filter.getHeight();
+ ssm.setMappingForPhyre2Model(false);
new Thread(new Runnable()
{
@Override
public void run()
{
- FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
- .getSelectedItem());
- String currentView = selectedFilterOpt.getView();
- if (currentView == VIEWS_FILTER)
- {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
int pdbIdColIndex = getResultTable().getColumn("PDB Id")
.getModelIndex();
int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
- .getModelIndex();
+ .getModelIndex();
int[] selectedRows = getResultTable().getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
String pdbIdStr = getResultTable().getValueAt(row,
- pdbIdColIndex)
- .toString();
+ pdbIdColIndex).toString();
SequenceI selectedSeq = (SequenceI) getResultTable()
- .getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
+ .getValueAt(row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = getFindEntry(pdbIdStr,
selectedSeq.getAllPDBEntries());
}
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+ }
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
}
- pdbEntriesToView[count++] = pdbEntry;
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_LOCAL_PDB)
- {
- int[] selectedRows = tbl_local_pdb.getSelectedRows();
- PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
+ else if (currentView == VIEWS_LOCAL_PDB)
+ {
+ int[] selectedRows = tbl_local_pdb.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
.getModelIndex();
- int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
- .getModelIndex();
- ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
- for (int row : selectedRows)
- {
- PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
- pdbIdColIndex);
- pdbEntriesToView[count++] = pdbEntry;
- SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- }
- SequenceI[] selectedSeqs = selectedSeqsToView
- .toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ssm, pdbEntriesToView, ap,
- selectedSeqs);
- }
- else if (currentView == VIEWS_ENTER_ID)
- {
- SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
- .getCmb_assSeq().getSelectedItem()).getSequence();
- if (userSelectedSeq != null)
- {
- selectedSequence = userSelectedSeq;
- }
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
+ {
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+ row, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ }
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
- String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = new PDBEntry();
+
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
if (pdbIdStr.split(":").length > 1)
{
- pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+ pdbEntry.setId(pdbIdStr.split(":")[0]);
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase());
}
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
- }
+ else
+ {
+ pdbEntry.setId(pdbIdStr);
+ }
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ }
- PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ssm, pdbEntriesToView, ap,
new SequenceI[] { selectedSequence });
}
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(selectedPdbFileName,
- jalview.io.AppletFormatAdapter.FILE,
+ PDBEntry fileEntry = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(selectedStructureFileName,
+ DataSourceType.FILE,
selectedSequence, true, Desktop.instance);
launchStructureViewer(ssm,
new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
- }
- mainFrame.dispose();
+ }
+ else if (currentView == VIEWS_PHYRE2_PREDICTION)
+ {
+ SequenceI userSelectedSeq = ((AssociateSeqOptions) phyre2InputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ if (userSelectedSeq != null)
+ {
+ selectedSequence = userSelectedSeq;
+ }
+ int templateColIndex = getPhyreResultTable()
+ .getColumn("Template")
+ .getModelIndex();
+ int[] selectedRows = getPhyreResultTable().getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int row : selectedRows)
+ {
+ String templateId = getPhyreResultTable().getValueAt(row,
+ templateColIndex).toString();
+ String structureFile = phyre2ResultDirectory + templateId
+ + ".pdb";
+ pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
+ .associateStructureWithSeq(structureFile,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+ }
+
+ final StructureSelectionManager ssm = ap
+ .getStructureSelectionManager();
+ ssm.setMappingForPhyre2Model(true);
+ final long progressSessionId = System.currentTimeMillis();
+ ssm.setProgressSessionId(progressSessionId);
+
+ SequenceI[] sequences = new SequenceI[] { selectedSequence };
+
+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
+ final StructureViewer sViewer = new StructureViewer(ssm);
+ if (pdbEntriesToView.length > 1)
+ {
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ for (SequenceI seq : sequences)
+ {
+ seqsMap.add(new SequenceI[] { seq });
+ }
+ SequenceI[][] collatedSeqs = seqsMap
+ .toArray(new SequenceI[0][0]);
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"));
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs, ap);
+ }
+ else
+ {
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_3d_structures_for",
+ pdbEntriesToView[0].getId()));
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, ap);
+ }
+ }
+ closeAction(preferredHeight);
}
}).start();
}
+ private String phyre2ResultDirectory;
+
+ @Override
+ public void predict3DModelWithPhyre2()
+ {
+ // TODO implement code for submitting sequence to Phyre2 service, and code
+ // for getting the result directory when the job completes, this is
+ // currently hard-wired to the directory of result for FER_CAPAN/1-144
+ phyre2ResultDirectory = "examples/testdata/phyre2results/56da5616b4559c93/";
+ String summaryhtml = phyre2ResultDirectory + "summary.html";
+ // TODO ditch HTML parsing once appropriated data file (i.e. JSON) for
+ // Phyre2 result summary is made available
+ List<Phyre2SummaryPojo> phyreResults = Phyre2Client
+ .parsePhyre2ResultSummaryTable(summaryhtml);
+ getPhyreResultTable()
+ .setModel(Phyre2Client.getTableModel(phyreResults));
+ Phyre2Client.configurePhyreResultTable(getPhyreResultTable());
+ }
+
private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
if (SiftsSettings.isMapWithSifts())
{
- // TODO: prompt user if there are lots of sequences without dbrefs.
- // It can take a long time if we need to fetch all dbrefs for all
- // sequences!
- ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+
for (SequenceI seq : sequences)
{
- if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
{
- seqsWithoutSourceDBRef.add(seq);
- continue;
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
}
+ }
+ if (seq.getPrimaryDBRefs().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
}
if (!seqsWithoutSourceDBRef.isEmpty())
{
public boolean isStructuresDiscovered()
{
- return structuresDiscovered;
- }
-
- public void setStructuresDiscovered(boolean structuresDiscovered)
- {
- this.structuresDiscovered = structuresDiscovered;
+ return discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty();
}
public Collection<FTSData> getDiscoveredStructuresSet()
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest
-.setSearchTerm(searchTerm + ")");
+ pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = PDBFTSRestClient.getInstance();
wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
git://source.jalview.org / jalview.git / blobdiff